On NameNode I see directory /etc/hadoop/conf.cloudera.yarn but it seems to be unused. For example, even though yarn.resourcemanager.address is set correctly in /etc/hadoop/conf.cloudera.yarn/yarn-site.xml I receive:

Your observations are correct and expected. The configuration differences are due to the logic used in Cloudera Manager's management of client configurations. Depending on what roles you have installed on each host, CM will determine the configuration files necessary for clients on those hosts. If you have a YARN role (NodeManager or Resource Manager) running on the same host as the NameNode, you will probably see the same alternative link to conf.cloudera.yarn.

This is because the YARN configuration will contain client files for YARN as well as HDFS.

If you wish, you can go to your YARN service in Cloudera Manager and click on the Instances subtab. Click Add new Role Instances and add a new role of "Gateway" to the NameNode host. Then, deploy client configuration. You will then see that the alternatives link will change to /etc/hadoop/conf.cloudera.yarn

Adding the Gateway Role will allow clients (not Services) to read the current client configuration.

Servers do not use the client configuration files in /etc. Rather, they use the configuration files deployed to the /var/run/cloudera-scm-agent/process directory when starting a service via Cloudera Manager.

I don't know if all of this will help you solve your problem since I didn't see what command you tried to run when the problem happened. If it doesn't help, please describe what the problem is and we'll help you.

Your observations are correct and expected. The configuration differences are due to the logic used in Cloudera Manager's management of client configurations. Depending on what roles you have installed on each host, CM will determine the configuration files necessary for clients on those hosts. If you have a YARN role (NodeManager or Resource Manager) running on the same host as the NameNode, you will probably see the same alternative link to conf.cloudera.yarn.

This is because the YARN configuration will contain client files for YARN as well as HDFS.

If you wish, you can go to your YARN service in Cloudera Manager and click on the Instances subtab. Click Add new Role Instances and add a new role of "Gateway" to the NameNode host. Then, deploy client configuration. You will then see that the alternatives link will change to /etc/hadoop/conf.cloudera.yarn

Adding the Gateway Role will allow clients (not Services) to read the current client configuration.

Servers do not use the client configuration files in /etc. Rather, they use the configuration files deployed to the /var/run/cloudera-scm-agent/process directory when starting a service via Cloudera Manager.

I don't know if all of this will help you solve your problem since I didn't see what command you tried to run when the problem happened. If it doesn't help, please describe what the problem is and we'll help you.

Thank you very much for your explanations. Especially I appreciated your clarification about service/client configuration difference and how to enable client configuration for yarn. It solves my issue, thanks a million.